1b8a

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{{Seed}}
 
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[[Image:1b8a.png|left|200px]]
 
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==ASPARTYL-TRNA SYNTHETASE==
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The line below this paragraph, containing "STRUCTURE_1b8a", creates the "Structure Box" on the page.
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<StructureSection load='1b8a' size='340' side='right'caption='[[1b8a]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1b8a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B8A FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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{{STRUCTURE_1b8a| PDB=1b8a | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b8a OCA], [https://pdbe.org/1b8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b8a RCSB], [https://www.ebi.ac.uk/pdbsum/1b8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b8a ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYD_THEKO SYD_THEKO] Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). Is specific for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude less efficiently than tRNA(Asp).<ref>PMID:12149259</ref> <ref>PMID:12660169</ref> <ref>PMID:12730374</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b8/1b8a_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1b8a ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of aspartyl-tRNA synthetase (AspRS) from Pyrococcus kodakaraensis was solved at 1.9 A resolution. The sequence and three-dimensional structure of the catalytic domain are highly homologous to those of eukaryotic AspRSs. In contrast, the N-terminal domain, whose function is to bind the tRNA anticodon, is more similar to that of eubacterial enzymes. Its structure explains the unique property of archaeal AspRSs of accommodating both tRNAAsp and tRNAAsn. Soaking the apo-enzyme crystals with ATP and aspartic acid both separately and together allows the adenylate formation to be followed. Due to the asymmetry of the dimeric enzyme in the crystalline state, different steps of the reaction could be visualized within the same crystal. Four different states of the aspartic acid activation reaction could thus be characterized, revealing the functional correlation of the observed conformational changes. The binding of the amino acid substrate induces movement of two invariant loops which secure the position of the peptidyl moiety for adenylate formation. An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaeal and eukaryotic AspRSs, but absent from the eubacterial enzymes.
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===ASPARTYL-TRNA SYNTHETASE===
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Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.,Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D EMBO J. 1998 Sep 1;17(17):5227-37. PMID:9724658<ref>PMID:9724658</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1b8a" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_9724658}}, adds the Publication Abstract to the page
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 9724658 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_9724658}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1B8A is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B8A OCA].
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[[Category: Thermococcus kodakarensis KOD1]]
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[[Category: Moras D]]
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==Reference==
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[[Category: Moulinier L]]
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Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation., Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D, EMBO J. 1998 Sep 1;17(17):5227-37. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9724658 9724658]
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[[Category: Schmitt E]]
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[[Category: Aspartate--tRNA ligase]]
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[[Category: Thierry J-C]]
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[[Category: Single protein]]
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[[Category: Thermococcus kodakarensis]]
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[[Category: Moras, D.]]
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[[Category: Moulinier, L.]]
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[[Category: Schmitt, E.]]
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[[Category: Thierry, J C.]]
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[[Category: Synthetase]]
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[[Category: Trna ligase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 18:32:40 2008''
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Current revision

ASPARTYL-TRNA SYNTHETASE

PDB ID 1b8a

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